I managed to dislodge her from the mines, after much experimentation - every major questline was complete or stuck without Fal's presence, but for no clear reason, progressing Grettel's questline until she moves to the library also triggered Fal to move back to the library.
(Thanks for the incredible games btw, AAA is one of my all time favourites, and I can't wait to get to QE and DreQ once I've finished this one)